838
Views
1
CrossRef citations to date
0
Altmetric
Research Article

Biochemistry-informed design selects potent siRNAs against SARS-CoV-2

, ORCID Icon, , ORCID Icon, ORCID Icon & ORCID Icon
Pages 272-280 | Accepted 08 May 2023, Published online: 04 Jun 2023

References

  • Ghildiyal M, Zamore PD. Small silencing RNAs: an expanding universe. Nat Rev Genet. 2009;10(2):94–108.
  • Carmell MA, Xuan Z, Zhang MQ, et al. The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev. 2002;16(21):2733–2742.
  • Elbashir SM, Lendeckel W, Tuschl T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 2001;15(2):188–200.
  • Elbashir SM, Martinez J, Patkaniowska A, et al. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. Embo J. 2001;20(23):6877–6888.
  • Llave C, Xie Z, Kasschau KD, et al. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science. 2002;297(5589):2053–2056.
  • Kasschau KD, Xie Z, Allen E, et al. P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function. Dev Cell. 2003;4(2):205–217.
  • Becker WR, Ober-Reynolds B, Jouravleva K, et al. High-throughput analysis reveals rules for target RNA binding and cleavage by AGO2. Mol Cell. 2019;75(4):741–755.
  • Holen T, Amarzguioui M, Wiiger MT, et al. Positional effects of short interfering RNAs targeting the human coagulation trigger tissue factor. Nucleic Acids Res. 2002;30(8):1757–1766.
  • Amarzguioui M, Holen T, Babaie E, et al. Tolerance for mutations and chemical modifications in a siRNA. Nucleic Acids Res. 2003;31(2):589–595.
  • Ding H, Schwarz DS, Keene A, et al. Selective silencing by RNAi of a dominant allele that causes amyotrophic lateral sclerosis. Aging Cell. 2003;2(4):209–217.
  • Haley B, Zamore PD. Kinetic analysis of the RNAi enzyme complex. Nat Struct Mol Biol. 2004;11(7):599–606.
  • Martinez J, Patkaniowska A, Urlaub H, et al. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell. 2002;110(5):563–574.
  • Meister G, Landthaler M, Patkaniowska A, et al. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol Cell. 2004;15(2):185–197.
  • Liu J, Carmell MA, Rivas FV, et al. Argonaute2 is the catalytic engine of mammalian RNAi. Science. 2004;305(5689):1437–1441.
  • Rivas FV, Tolia NH, Song JJ, et al. Purified Argonaute2 and an siRNA form recombinant human RISC. Nat Struct Mol Biol. 2005;12(4):340–349.
  • Park MS, Phan HD, Busch F, et al. Human Argonaute3 has slicer activity. Nucleic Acids Res. 2017;45(20):11867–11877.
  • Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell. 2009;136(2):215–233.
  • Hutvágner G, Zamore PD. A microRNA in a multiple-turnover RNAi enzyme complex. Science. 2002;297(5589):2056–2060.
  • Yekta S, Shih IH, Bartel DP. MicroRNA-directed cleavage of HOXB8 mRNA. Science. 2004;304(5670):594–596.
  • Davis E, Caiment F, Tordoir X, et al. RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg11 locus. Curr Biol. 2005;15(8):743–749.
  • Shin C, Nam JW, Farh KK, et al. Expanding the microRNA targeting code: functional sites with centered pairing. Mol Cell. 2010;38(6):789–802.
  • Karginov FV, Cheloufi S, Chong MM, et al. Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases. Mol Cell. 2010;38(6):781–788.
  • Iwakawa HO, Tomari Y. The functions of microRNAs: mRNA decay and translational repression. Trends Cell Biol. 2015;25(11):651–665.
  • Silva JM, Hammond SM, Hannon GJ. RNA interference: a promising approach to antiviral therapy? Trends Mol Med. 2002;8(11):505–508.
  • Wood H. FDA approves patisiran to treat hereditary transthyretin amyloidosis. Nat Rev Neurol. 2018;14(10):570.
  • Scott LJ. Givosiran: first approval. Drugs. 2020;80(3):335–339.
  • Scott LJ, Keam SJ. Lumasiran: first approval. Drugs. 2021;81(2):277–282.
  • Lamb YN. Inclisiran: first approval. Drugs. 2021;81(3):389–395.
  • Keam SJ. Vutrisiran: first approval. Drugs. 2022;82(13):1419–1425.
  • Qiu Y, Lam JK, Leung SW, et al. Delivery of RNAi therapeutics to the airways — from bench to bedside. Molecules. 2016;21(9):1249.
  • Wu F, Zhao S, Yu B, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579(7798):265–269.
  • Elbe S, Buckland-Merrett G. Data, disease and diplomacy: GISAID’s innovative contribution to global health. Glob Chall. 2017;1(1):33–46.
  • Bartel DP. Metazoan microRNAs. Cell. 2018;173(1):20–51.
  • De N, Young L, Lau PW, et al. Highly complementary target RNAs promote release of guide RNAs from human Argonaute2. Mol Cell. 2013;50(3):344–355.
  • Chable-Bessia C, Boull C, Neyret A, et al. Low selectivity indices of ivermectin and macrocyclic lactones on SARS-CoV-2 replication in vitro. COVID. 2022;2(1):60–75.
  • Laplantine E, Chable-Bessia C, Oudin A, et al. The FDA-approved drug Auranofin has a dual inhibitory effect on SARS-CoV-2 entry and NF-κB signaling. iScience. 2022;25(10):105066.
  • Ambike S, Cheng CC, Feuerherd M, et al. Targeting genomic SARS-CoV-2 RNA with siRNAs allows efficient inhibition of viral replication and spread. Nucleic Acids Res. 2022;50(1):333–349.
  • Tafer H, Ameres SL, Obernosterer G, et al. The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol. 2008;26(5):578–583.
  • Schwarz DS, Ding H, Kennington L, et al. Designing siRNA that distinguish between genes that differ by a single nucleotide. PLoS Genet. 2006;2(9):e140.
  • Wee LM, Flores-Jasso CF, Salomon WE, et al. Argonaute divides its RNA guide into domains with distinct functions and RNA-binding properties. Cell. 2012;151(5):1055–1067.
  • Schirle NT, Sheu-Gruttadauria J, MacRae IJ. Structural basis for microRNA targeting. Science. 2014;346(6209):608–613.
  • Frank F, Sonenberg N, Nagar B. Structural basis for 5’-nucleotide base-specific recognition of guide RNA by human AGO2. Nature. 2010;465(7299):818–822.
  • Hu HY, Yan Z, Xu Y, et al. Sequence features associated with microRNA strand selection in humans and flies. BMC Genomics. 2009;10:413.
  • Arvey A, Larsson E, Sander C, et al. Target mRNA abundance dilutes microRNA and siRNA activity. Mol Syst Biol. 2010;6(1):363.
  • Birmingham A, Anderson EM, Reynolds A, et al. 3’ UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat Methods. 2006;3(3):199–204.
  • Dang VT, Kassahn KS, Marcos AE, et al. Identification of human haploinsufficient genes and their genomic proximity to segmental duplications. Eur JHum Genet. 2008;16(11):1350–1357.
  • Aza-Blanc P, Cooper CL, Wagner K, et al. Identification of modulators of TRAIL-induced apoptosis via RNAi-based phenotypic screening. Mol Cell. 2003;12(3):627–637.
  • Schwarz DS, Hutvágner G, Du T, et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell. 2003;115(2):199–208.
  • Khvorova A, Reynolds A, Jayasena SD. Functional siRNAs and miRNAs exhibit strand bias. Cell. 2003;115(2):209–216.
  • Nykänen A, Haley B, Zamore PD. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell. 2001;107(3):309–321.
  • Harcourt J, Tamin A, Lu X, et al. Severe acute respiratory syndrome coronavirus 2 from patient with coronavirus disease, United States. Emerg Infect Dis. 2020;26(6):1266–1273.
  • Blanco-Melo D, Nilsson-Payant BE, Liu WC, et al. Imbalanced host response to SARS-CoV-2 drives development of COVID-19. Cell. 2020;181(5):1036–1045.
  • Khaitov M, Nikonova A, Shilovskiy I, et al. Silencing of SARS-CoV-2 with modified siRNA-peptide dendrimer formulation. Allergy. 2021;76(9):2840–2854.
  • Idris A, Davis A, Supramaniam A, et al. A SARS-CoV-2 targeted siRNA-nanoparticle therapy for COVID-19. Mol Ther. 2021;29(7):2219–2226.
  • Tolksdorf B, Nie C, Niemeyer D, et al. Inhibition of SARS-CoV-2 replication by a small interfering RNA targeting the leader sequence. Viruses. 2021;13(10):2030.
  • Niktab I, Haghparast M, Beigi MH, et al. Design of advanced siRNA therapeutics for the treatment of COVID-19. Meta Gene. 2021;29:100910.
  • Sohrab SS, El-Kafrawy SA, Azhar EI. In silico prediction and experimental evaluation of potential siRNAs against SARS-CoV-2 inhibition in Vero E6 cells. J King Saud Univ Sci. 2022;34(4):102049.
  • Yogev O, Weissbrod O, Battistoni G, et al. From a genome-wide screen of RNAi molecules against SARS-CoV-2 to a validated broad-spectrum and potent prophylaxis. Commun Biol. 2023;6(1):277.
  • Sohrab SS, El-Kafrawy SA, Azhar EI. Effect of in silico predicted and designed potential siRNAs on inhibition of SARS-CoV-2 in HEK-293 cells. J King Saud Univ Sci. 2022;34(4):101965.
  • Friedrich M, Pfeifer G, Binder S, et al. Selection and validation of siRNAs preventing uptake and replication of SARS-CoV-2. Front Bioeng Biotechnol. 2022;10:801870.
  • Chang YC, Yang CF, Chen YF, et al. A siRNA targets and inhibits a broad range of SARS-CoV-2 infections including Delta variant. EMBO Mol Med. 2022;14(4):e15298.
  • Becker J, Stanifer ML, Leist SR, et al. Ex vivo and in vivo suppression of SARS-CoV-2 with combinatorial AAV/RNAi expression vectors. Mol Ther. 2022;30(5):2005–2023.
  • Nabiabad HS, Amini M, Demirdas S. Specific delivering of RNAi using Spike’s aptamer-functionalized lipid nanoparticles for targeting SARS-CoV-2: a strong anti-Covid drug in a clinical case study. Chem Biol Drug Des. 2022;99(2):233–246.
  • Horby P, Lim WS, Emberson JR, et al. Dexamethasone in hospitalized patients with Covid-19. N Engl J Med. 2021;384(8):693–704.
  • Jayk Bernal A, Gomes da Silva MM, Musungaie DB, et al. Molnupiravir for oral treatment of Covid-19 in nonhospitalized patients. N Engl J Med. 2022;386(6):509–520.
  • Gottlieb RL, Nirula A, Chen P, et al. Effect of bamlanivimab as monotherapy or in combination with etesevimab on viral load in patients with mild to moderate COVID-19: a randomized clinical trial. JAMA. 2021;325(7):632–644.
  • Rockx B, Kuiken T, Herfst S, et al. Comparative pathogenesis of COVID-19, MERS, and SARS in a nonhuman primate model. Science. 2020;368(6494):1012–1015.